1-41511257-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_024503.5(HIVEP3):c.6415G>A(p.Glu2139Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000442 in 1,602,634 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.0022 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00025 ( 5 hom. )
Consequence
HIVEP3
NM_024503.5 missense
NM_024503.5 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 0.612
Genes affected
HIVEP3 (HGNC:13561): (HIVEP zinc finger 3) This gene encodes a member of the human immunodeficiency virus type 1 enhancer-binding protein family. Members of this protein family contain multiple zinc finger and acid-rich (ZAS) domains and serine-threonine rich regions. This protein acts as a transcription factor and is able to regulate nuclear factor kappaB-mediated transcription by binding the kappaB motif in target genes. This protein also binds the recombination signal sequence that flanks the V, D, and J regions of immunoglobulin and T-cell receptors. Alternate splicing results in both coding and non-coding transcript variants. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.003950864).
BP6
Variant 1-41511257-C-T is Benign according to our data. Variant chr1-41511257-C-T is described in ClinVar as [Benign]. Clinvar id is 3035562.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High Homozygotes in GnomAdExome4 at 5 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIVEP3 | NM_024503.5 | c.6415G>A | p.Glu2139Lys | missense_variant | 9/9 | ENST00000372583.6 | |
HIVEP3 | NM_001127714.3 | c.6412G>A | p.Glu2138Lys | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIVEP3 | ENST00000372583.6 | c.6415G>A | p.Glu2139Lys | missense_variant | 9/9 | 1 | NM_024503.5 | P5 | |
HIVEP3 | ENST00000372584.5 | c.6412G>A | p.Glu2138Lys | missense_variant | 8/8 | 1 | A2 | ||
HIVEP3 | ENST00000643665.1 | c.6412G>A | p.Glu2138Lys | missense_variant | 8/8 | A2 | |||
HIVEP3 | ENST00000460604.1 | n.1342G>A | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00225 AC: 342AN: 152114Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000678 AC: 162AN: 238854Hom.: 0 AF XY: 0.000488 AC XY: 63AN XY: 129112
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GnomAD4 exome AF: 0.000253 AC: 367AN: 1450402Hom.: 5 Cov.: 33 AF XY: 0.000190 AC XY: 137AN XY: 719958
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GnomAD4 genome AF: 0.00225 AC: 342AN: 152232Hom.: 1 Cov.: 32 AF XY: 0.00214 AC XY: 159AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
HIVEP3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 09, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
.;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M;.
MutationTaster
Benign
N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
.;N;N
REVEL
Benign
Sift
Benign
.;D;D
Sift4G
Benign
.;T;T
Polyphen
P;P;P
Vest4
0.090, 0.13
MVP
0.28
MPC
0.25
ClinPred
T
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at